Understanding the behavior of large language models (LLMs) is crucial for ensuring their safe and reliable use. However, existing explainable AI (XAI) methods for LLMs primarily rely on word-level explanations, which are often computationally inefficient and misaligned with human reasoning processes. Moreover, these methods often treat explanation as a one-time output, overlooking its inherently interactive and iterative nature. In this paper, we present LLM Analyzer, an interactive visualization system that addresses these limitations by enabling intuitive and efficient exploration of LLM behaviors through counterfactual analysis. Our system features a novel algorithm that generates fluent and semantically meaningful counterfactuals via targeted removal and replacement operations at user-defined levels of granularity. These counterfactuals are used to compute feature attribution scores, which are then integrated with concrete examples in a table-based visualization, supporting dynamic analysis of model behavior. A user study with LLM practitioners and interviews with experts demonstrate the system's usability and effectiveness, emphasizing the importance of involving humans in the explanation process as active participants rather than passive recipients.

Lucas Monteiro Paes, Dennis Wei, Hyo Jin Do, Hendrik Strobelt, Ronny Luss, Amit Dhurandhar, Manish Nagireddy, Karthikeyan Natesan Ramamurthy, Prasanna Sattigeri, Werner Geyer, Soumya Ghosh. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

CHI ’25, Yokohama, Japan

Vision Transformers (ViTs), with their ability to model long-range dependencies through self-attention mechanisms, have become a standard architecture in computer vision. However, the interpretability of these models remains a challenge. To address this, we propose LeGrad, an explainability method specifically designed for ViTs. LeGrad computes the gradient with respect to the attention maps of ViT layers, considering the gradient itself as the explainability signal. We aggregate the signal over all layers, combining the activations of the last as well as intermediate tokens to produce the merged explainability map. This makes LeGrad a conceptually simple and an easy-to-implement tool for enhancing the transparency of ViTs. We evaluate LeGrad in challenging segmentation, perturbation, and open-vocabulary settings, showcasing its versatility compared to other SotA explainability methods demonstrating its superior spatial fidelity and robustness to perturbations. A demo and the code is available at https://github.com/WalBouss/LeGrad.

Large Language Models (LLMs) are notorious for blending fact with fiction and generating non-factual content, known as hallucinations. To address this challenge, we propose an interactive system that helps users gain insight into the reliability of the generated text. Our approach is based on the idea that the self-consistency of multiple samples generated by the same LLM relates to its confidence in individual claims in the generated texts. Using this idea, we design RELIC, an interactive system that enables users to investigate and verify semantic-level variations in multiple long-form responses. This allows users to recognize potentially inaccurate information in the generated text and make necessary corrections. From a user study with ten participants, we demonstrate that our approach helps users better verify the reliability of the generated text. We further summarize the design implications and lessons learned from this research for future studies of reliable human-LLM interactions.

This research explores integration of a Large Language Model (LLM) fine-tuned to conversationally control the user interface (UI) for a Semantic Automation Layer (SAL). We condense SAL capabilities from prior work and prioritize with business analysts and data engineers via a Kano model, before implementing a prototypical UI. We augment the UI with our conversational engine and propose In-situ Prompt Engineering and learn from Human Feedback to smoothen the interaction and manipulation of UI through natural language commands. To evaluate the efficacy and usability of conversational control in various use-case scenarios, we conduct and report on an empirical interaction design user study. Our findings provide evidence supporting enhanced user engagement and satisfaction. We also observe significant increase of trust in AI after working with our conversational UI. This work generates areas for further refinement and research towards more intelligent, highly-integrated conversational UIs even beyond our application within Semantic Automation. We discuss our findings and point out next steps paving the way for future research and development in creating more intuitive and adaptive user interfaces.

Dense Associative Memories are high storage capacity variants of the Hopfield networks that are capable of storing a large number of memory patterns in the weights of the network of a given size. Their common formulations typically require storing each pattern in a separate set of synaptic weights, which leads to the increase of the number of synaptic weights when new patterns are introduced. In this work we propose an alternative formulation of this class of models using random features, commonly used in kernel methods. In this formulation the number of network's parameters remains fixed. At the same time, new memories can be added to the network by modifying existing weights. We show that this novel network closely approximates the energy function and dynamics of conventional Dense Associative Memories and shares their desirable computational properties.

Many papers make claims about specific visualization techniques that are said to enhance or calibrate trust in AI systems. But a design choice that enhances trust in some cases appears to damage it in others. In this paper, we explore this inherent duality through an analogy with "knobs". Turning a knob too far in one direction may result in under-trust, too far in the other, over-trust or, turned up further still, in a confusing distortion. While the designs or so-called "knobs" are not inherently evil, they can be misused or used in an adversarial context and thereby manipulated to mislead users or promote unwarranted levels of trust in AI systems. When a visualization that has no meaningful connection with the underlying model or data is employed to enhance trust, we refer to the result as "trust junk." From a review of 65 papers, we identify nine commonly made claims about trust calibration. We synthesize them into a framework of knobs that can be used for good or "evil," and distill our findings into observed pitfalls for the responsible design of human-AI systems.

Diffusion-based generative models’ impressive ability to create convincing images has garnered global attention. However, their complex structures and operations often pose challenges for non-experts to grasp. We present Diffusion Explainer, the first interactive visualization tool that explains how Stable Diffusion transforms text prompts into images. Diffusion Explainer tightly integrates a visual overview of Stable Diffusion’s complex structure with explanations of the underlying operations. By comparing image generation of prompt variants, users can discover the impact of keyword changes on image generation. A 56-participant user study demonstrates that Diffusion Explainer offers substantial learning benefits to non-experts. Our tool has been used by over 10,300 users from 124 countries at https://poloclub.github.io/diffusion-explainer/.

Our work combines aspects of three promising paradigms in machine learning, namely, attention mechanism, energy-based models, and associative memory. Attention is the power-house driving modern deep learning successes, but it lacks clear theoretical foundations. Energy-based models allow a principled approach to discriminative and generative tasks, but the design of the energy functional is not straightforward. At the same time, Dense Associative Memory models or Modern Hopfield Networks have a well-established theoretical foundation, and allow an intuitive design of the energy function. We propose a novel architecture, called the Energy Transformer (or ET for short), that uses a sequence of attention layers that are purposely designed to minimize a specifically engineered energy function, which is responsible for representing the relationships between the tokens. In this work, we introduce the theoretical foundations of ET, explore its empirical capabilities using the image completion task, and obtain strong quantitative results on the graph anomaly detection and graph classification tasks.

Abstract Euler diagrams are a popular technique to visualize set‐typed data. However, creating diagrams using simple shapes remains a challenging problem for many complex, real‐life datasets. To solve this, we propose RectEuler: a flexible, fully‐automatic method using rectangles to create Euler‐like diagrams. We use an efficient mixed‐integer optimization scheme to place set labels and element representatives (e.g., text or images) in conjunction with rectangles describing the sets. By defining appropriate constraints, we adhere to well‐formedness properties and aesthetic considerations. If a dataset cannot be created within a reasonable time or at all, we iteratively split the diagram into multiple components until a drawable solution is found. Redundant encoding of the set membership using dots and set lines improves the readability of the diagram. Our web tool lets users see how the layout changes throughout the optimization process and provides interactive explanations. For evaluation, we perform quantitative and qualitative analysis across different datasets and compare our method to state‐of‐the‐art Euler diagram generation methods.

State-of-the-art neural language models can now be used to solve ad-hoc language tasks through zero-shot prompting without the need for supervised training. This approach has gained popularity in recent years, and researchers have demonstrated prompts that achieve strong accuracy on specific NLP tasks. However, finding a prompt for new tasks requires experimentation. Different prompt templates with different wording choices lead to significant accuracy differences. PromptIDE allows users to experiment with prompt variations, visualize prompt performance, and iteratively optimize prompts. We developed a workflow that allows users to first focus on model feedback using small data before moving on to a large data regime that allows empirical grounding of promising prompts using quantitative measures of the task. The tool then allows easy deployment of the newly created ad-hoc models. We demonstrate the utility of PromptIDE (demo: http://prompt.vizhub.ai) and our workflow using several real-world use cases.

Presents the welcome message from the VIS 2022 General Chairs.

Saliency methods — techniques to identify the importance of input features on a model’s output — are a common step in understanding neural network behavior. However, interpreting saliency requires tedious manual inspection to identify and aggregate patterns in model behavior, resulting in ad hoc or cherry-picked analysis. To address these concerns, we present Shared Interest: metrics for comparing model reasoning (via saliency) to human reasoning (via ground truth annotations). By providing quantitative descriptors, Shared Interest enables ranking, sorting, and aggregating inputs, thereby facilitating large-scale systematic analysis of model behavior. We use Shared Interest to identify eight recurring patterns in model behavior, such as cases where contextual features or a subset of ground truth features are most important to the model. Working with representative real-world users, we show how Shared Interest can be used to decide if a model is trustworthy, uncover issues missed in manual analyses, and enable interactive probing.

Classifiers are among the most widely used supervised machine learning algorithms. Many classification models exist, and choosing the right one for a given task is difficult. During model selection and debugging, data scientists need to assess classifiers' performances, evaluate their learning behavior over time, and compare different models. Typically, this analysis is based on single-number performance measures such as accuracy. A more detailed evaluation of classifiers is possible by inspecting class errors. The confusion matrix is an established way for visualizing these class errors, but it was not designed with temporal or comparative analysis in mind. More generally, established performance analysis systems do not allow a combined temporal and comparative analysis of class-level information. To address this issue, we propose ConfusionFlow, an interactive, comparative visualization tool that combines the benefits of class confusion matrices with the visualization of performance characteristics over time. ConfusionFlow is model-agnostic and can be used to compare performances for different model types, model architectures, and/or training and test datasets. We demonstrate the usefulness of ConfusionFlow in a case study on instance selection strategies in active learning. We further assess the scalability of ConfusionFlow and present a use case in the context of neural network pruning.

Table2Text systems generate textual output based on structured data utilizing machine learning. These systems are essential for fluent natural language interfaces in tools such as virtual assistants; however, left to generate freely these ML systems often produce misleading or unexpected outputs. GenNI (Generation Negotiation Interface) is an interactive visual system for high-level human-AI collaboration in producing descriptive text. The tool utilizes a deep learning model designed with explicit control states. These controls allow users to globally constrain model generations, without sacrificing the representation power of the deep learning models. The visual interface makes it possible for users to interact with AI systems following a Refine-Forecast paradigm to ensure that the generation system acts in a manner human users find suitable. We report multiple use cases on two experiments that improve over uncontrolled generation approaches, while at the same time providing fine-grained control. A demo and source code are available at https://genni.vizhub.ai.

The spread of infectious diseases such as COVID-19 presents many challenges to healthcare systems and infrastructures across the world, exacerbating inequalities and leaving the world's most vulnerable populations most affected. Given their density and available infrastructure, refugee and internally displaced person (IDP) settlements can be particularly susceptible to disease spread. In this paper we present an agent-based modeling approach to simulating the spread of disease in refugee and IDP settlements under various non-pharmaceutical intervention strategies. The model, based on the June open-source framework, is informed by data on geography, demographics, comorbidities, physical infrastructure and other parameters obtained from real-world observations and previous literature. The development and testing of this approach focuses on the Cox's Bazar refugee settlement in Bangladesh, although our model is designed to be generalizable to other informal settings. Our findings suggest the encouraging self-isolation at home of mild to severe symptomatic patients, as opposed to the isolation of all positive cases in purpose-built isolation and treatment centers, does not increase the risk of secondary infection meaning the centers can be used to provide hospital support to the most intense cases of COVID-19. Secondly we find that mask wearing in all indoor communal areas can be effective at dampening viral spread, even with low mask efficacy and compliance rates. Finally, we model the effects of reopening learning centers in the settlement under various mitigation strategies. For example, a combination of mask wearing in the classroom, halving attendance regularity to enable physical distancing, and better ventilation can almost completely mitigate the increased risk of infection which keeping the learning centers open may cause. These modeling efforts are being incorporated into decision making processes to inform future planning, and further exercises should be carried out in similar geographies to help protect those most vulnerable.

The novel nature of SARS-CoV-2 calls for the development of efficient de novo drug design approaches. In this study, we propose an end-to-end framework, named CogMol (Controlled Generation of Molecules), for designing new drug-like small molecules targeting novel viral proteins with high affinity and off-target selectivity. CogMol combines adaptive pre-training of a molecular SMILES Variational Autoencoder (VAE) and an efficient multi-attribute controlled sampling scheme that uses guidance from attribute predictors trained on latent features. To generate novel and optimal drug-like molecules for unseen viral targets, CogMol leverages a protein-molecule binding affinity predictor that is trained using SMILES VAE embeddings and protein sequence embeddings learned unsupervised from a large corpus. We applied the CogMol framework to three SARS-CoV-2 target proteins: main protease, receptor-binding domain of the spike protein, and non-structural protein 9 replicase. The generated candidates are novel at both the molecular and chemical scaffold levels when compared to the training data. CogMol also includes insilico screening for assessing toxicity of parent molecules and their metabolites with a multi-task toxicity classifier, synthetic feasibility with a chemical retrosynthesis predictor, and target structure binding with docking simulations. Docking reveals favorable binding of generated molecules to the target protein structure, where 87--95\% of high affinity molecules showed docking free energy $<$ -6 kcal/mol. When compared to approved drugs, the majority of designed compounds show low predicted parent molecule and metabolite toxicity and high predicted synthetic feasibility. In summary, CogMol can handle multi-constraint design of synthesizable, low-toxic, drug-like molecules with high target specificity and selectivity, even to novel protein target sequences, and does not need target-dependent fine-tuning of the framework or target structure information.

The performance of deep learning models is dependent on the precise configuration of many layers and parameters. However, there are currently few systematic guidelines for how to configure a successful model. This means model builders often have to experiment with different configurations by manually programming different architectures (which is tedious and time consuming) or rely on purely automated approaches to generate and train the architectures (which is expensive). In this paper, we present Rapid Exploration of Model Architectures and Parameters, or REMAP, a visual analytics tool that allows a model builder to discover a deep learning model quickly via exploration and rapid experimentation of neural network architectures. In REMAP, the user explores the large and complex parameter space for neural network architectures using a combination of global inspection and local experimentation. Through a visual overview of a set of models, the user identifies interesting clusters of architectures. Based on their findings, the user can run ablation and variation experiments to identify the effects of adding, removing, or replacing layers in a given architecture and generate new models accordingly. They can also handcraft new models using a simple graphical interface. As a result, a model builder can build deep learning models quickly, efficiently, and without manual programming. We inform the design of REMAP through a design study with four deep learning model builders. Through a use case, we demonstrate that REMAP allows users to discover performant neural network architectures efficiently using visual exploration and user-defined semi-automated searches through the model space.

Automation of tasks can have critical consequences when humans lose agency over decision processes. Deep learning models are particularly susceptible since current black-box approaches lack explainable reasoning. We argue that both the visual interface and model structure of deep learning systems need to take into account interaction design. We propose a framework of collaborative semantic inference (CSI) for the co-design of interactions and models to enable visual collaboration between humans and algorithms. The approach exposes the intermediate reasoning process of models which allows semantic interactions with the visual metaphors of a problem, which means that a user can both understand and control parts of the model reasoning process. We demonstrate the feasibility of CSI with a co-designed case study of a document summarization system.

Despite the success of Generative Adversarial Networks (GANs), mode collapse remains a serious issue during GAN training. To date, little work has focused on understanding and quantifying which modes have been dropped by a model. In this work, we visualize mode collapse at both the distribution level and the instance level. First, we deploy a semantic segmentation network to compare the distribution of segmented objects in the generated images with the target distribution in the training set. Differences in statistics reveal object classes that are omitted by a GAN. Second, given the identified omitted object classes, we visualize the GAN's omissions directly. In particular, we compare specific differences between individual photos and their approximate inversions by a GAN. To this end, we relax the problem of inversion and solve the tractable problem of inverting a GAN layer instead of the entire generator. Finally, we use this framework to analyze several recent GANs trained on multiple datasets and identify their typical failure cases.

Despite the recent success of GANs in synthesizing images conditioned on inputs such as a user sketch, text, or semantic labels, manipulating the high-level attributes of an existing natural photograph with GANs is challenging for two reasons. First, it is hard for GANs to precisely reproduce an input image. Second, after manipulation, the newly synthesized pixels often do not fit the original image. In this paper, we address these issues by adapting the image prior learned by GANs to image statistics of an individual image. Our method can accurately reconstruct the input image and synthesize new content, consistent with the appearance of the input image. We demonstrate our interactive system on several semantic image editing tasks, including synthesizing new objects consistent with background, removing unwanted objects, and changing the appearance of an object. Quantitative and qualitative comparisons against several existing methods demonstrate the effectiveness of our method.

Neural sequence-to-sequence models have proven to be accurate and robust for many sequence prediction tasks, and have become the standard approach for automatic translation of text. The models work with a five-stage blackbox pipeline that begins with encoding a source sequence to a vector space and then decoding out to a new target sequence. This process is now standard, but like many deep learning methods remains quite difficult to understand or debug. In this work, we present a visual analysis tool that allows interaction and "what if"-style exploration of trained sequence-to-sequence models through each stage of the translation process. The aim is to identify which patterns have been learned, to detect model errors, and to probe the model with counterfactual scenario. We demonstrate the utility of our tool through several real-world sequence-to-sequence use cases on large-scale models.

Motivation: Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the Saccharomyces cerevisiae and Escherichia coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. Results: We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S.cerevisiae and E.coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution. Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (P-value < 10-10) and -0.46 (P-value < 10-10) for S.cerevisiae and E.coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant. Availability and implementation: ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

Bioinformatics (2018) https://doi.org/10.1093/bioinformatics/bty370 The publisher wishes to apologize for a mistake in Figure 1 in the above manuscript. The figure appears correctly below: The ProteomeVis web app after exploration has occurred. Hovering over asterisks located in the top-right corner of each panel opens an informational window. Pressing the help button (question mark symbol) located to the right of the Control Strip (A) leads to a quick tour. Alphabetical labels (A–E) are added to each component of ProteomeVis in this figure to introduce the tool in the text The paper has been corrected online.

Recurrent neural networks, and in particular long short-term memory (LSTM) networks, are a remarkably effective tool for sequence modeling that learn a dense black-box hidden representation of their sequential input. Researchers interested in better understanding these models have studied the changes in hidden state representations over time and noticed some interpretable patterns but also significant noise. In this work, we present LSTMVis, a visual analysis tool for recurrent neural networks with a focus on understanding these hidden state dynamics. The tool allows users to select a hypothesis input range to focus on local state changes, to match these states changes to similar patterns in a large data set, and to align these results with structural annotations from their domain. We show several use cases of the tool for analyzing specific hidden state properties on dataset containing nesting, phrase structure, and chord progressions, and demonstrate how the tool can be used to isolate patterns for further statistical analysis. We characterize the domain, the different stakeholders, and their goals and tasks. Long-term usage data after putting the tool online revealed great interest in the machine learning community.

High-throughput and high-content screening enables large scale, cost-effective experiments in which cell cultures are exposed to a wide spectrum of drugs. The resulting multivariate data sets have a large but shallow hierarchical structure. The deepest level of this structure describes cells in terms of numeric features that are derived from image data. The subsequent level describes enveloping cell cultures in terms of imposed experiment conditions (exposure to drugs). We present Screenit, a visual analysis approach designed in close collaboration with screening experts. Screenit enables the navigation and analysis of multivariate data at multiple hierarchy levels and at multiple levels of detail. Screenit integrates the interactive modeling of cell physical states (phenotypes) and the effects of drugs on cell cultures (hits). In addition, quality control is enabled via the detection of anomalies that indicate low-quality data, while providing an interface that is designed to match workflows of screening experts. We demonstrate analyses for a real-world data set, CellMorph, with 6 million cells across 20,000 cell cultures.

Information hierarchies are difficult to express when real-world space or time constraints force traversing the hierarchy in linear presentations, such as in educational books and classroom courses. We present booc.io, which allows linear and non-linear presentation and navigation of educational concepts and material. To support a breadth of material for each concept, booc.io is Web based, which allows adding material such as lecture slides, book chapters, videos, and LTIs. A visual interface assists the creation of the needed hierarchical structures. The goals of our system were formed in expert interviews, and we explain how our design meets these goals. We adapt a real-world course into booc.io, and perform introductory qualitative evaluation with students.

Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.

Semi-automatic text analysis involves manual inspection of text. Often, different text annotations (like part-of-speech or named entities) are indicated by using distinctive text highlighting techniques. In typesetting there exist well-known formatting conventions, such as bold typeface, italics, or background coloring, that are useful for highlighting certain parts of a given text. Also, many advanced techniques for visualization and highlighting of text exist; yet, standard typesetting is common, and the effects of standard typesetting on the perception of text are not fully understood. As such, we surveyed and tested the effectiveness of common text highlighting techniques, both individually and in combination, to discover how to maximize pop-out effects while minimizing visual interference between techniques. To validate our findings, we conducted a series of crowdsourced experiments to determine: i) a ranking of nine commonly-used text highlighting techniques; ii) the degree of visual interference between pairs of text highlighting techniques; iii) the effectiveness of techniques for visual conjunctive search. Our results show that increasing font size works best as a single highlighting technique, and that there are significant visual interferences between some pairs of highlighting techniques. We discuss the pros and cons of different combinations as a design guideline to choose text highlighting techniques for text viewers.

Presents corrections for the paper, "Guidelines for effective usage of text highlighting techniques," (Strobelt, H., et al), IEEE Trans. Vis. Comput.Graph., vol. 22, no. 1, pp. 489-498, Jan. 2016.

Abstract We present an analysis and visualization method for computing what distinguishes a given document collection from others. We determine topics that discriminate a subset of collections from the remaining ones by applying probabilistic topic modeling and subsequently approximating the two relevant criteria distinctiveness and characteristicness algorithmically through a set of heuristics. Furthermore, we suggest a novel visualization method called DiTop‐View, in which topics are represented by glyphs (topic coins) that are arranged on a 2D plane. Topic coins are designed to encode all information necessary for performing comparative analyses such as the class membership of a topic, its most probable terms and the discriminative relations. We evaluate our topic analysis using statistical measures and a small user experiment and present an expert case study with researchers from political sciences analyzing two real‐world datasets.

We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains.

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets. At its core ConTour lists all items of each dataset in a column. Relationships between the columns are revealed through interaction: selecting one or multiple items in one column highlights and re-sorts the items in other columns. Filters based on relationships enable drilling down into the large data space. To identify interesting items in the first place, ConTour employs advanced sorting strategies, including strategies based on connectivity strength and uniqueness, as well as sorting based on item attributes. ConTour also introduces interactive nesting of columns, a powerful method to show the related items of a child column for each item in the parent column. Within the columns, ConTour shows rich attribute data about the items as well as information about the connection strengths to other datasets. Finally, ConTour provides a number of detail views, which can show items from multiple datasets and their associated data at the same time. We demonstrate the utility of our system in case studies conducted with a team of chemical biologists, who investigate the effects of chemical compounds on cells and need to understand the underlying mechanisms.

We present HiTSEE (High-Throughput Screening Exploration Environment), a visualization tool for the analysis of large chemical screens used to examine biochemical processes. The tool supports the investigation of structure-activity relationships (SAR analysis) and, through a flexible interaction mechanism, the navigation of large chemical spaces. Our approach is based on the projection of one or a few molecules of interest and the expansion around their neighborhood and allows for the exploration of large chemical libraries without the need to create an all encompassing overview of the whole library. We describe the requirements we collected during our collaboration with biologists and chemists, the design rationale behind the tool, and two case studies on different datasets. The described integration (HiTSEE KNIME) into the KNIME platform allows additional flexibility in adopting our approach to a wide range of different biochemical problems and enables other research groups to use HiTSEE.

Abstract Document reader applications usually offer an overview of the layout for each page as thumbnail views. Reading the text in these becomes impossible when the font size becomes very small. We improve the readability of these thumbnails using a distortion method, which retains a readable font size of interesting text while shrinking less interesting text further. In contrast to existing approaches, our method preserves the global layout of a page and is able to show context around important terms. We evaluate our technique and show application examples.

Abstract When representing 2D data points with spacious objects such as labels, overlap can occur. We present a simple algorithm which modifies the (Mani‐) Wordle idea with scan‐line based techniques to allow a better placement. We give an introduction to common placement techniques from different fields and compare our method to these techniques w.r.t. euclidean displacement, changes in orthogonal ordering as well as shape and size preservation. Especially in dense scenarios our method preserves the overall shape better than known techniques and allows a good trade‐off between the other measures. Applications on real world data are given and discussed.

We propose a technique that allows straight-line graph drawings to be rendered interactively with adjustable level of detail. The approach consists of a novel combination of edge cumulation with density-based node aggregation and is designed to exploit common graphics hardware for speed. It operates directly on graph data and does not require precomputed hierarchies or meshes. As proof of concept, we present an implementation that scales to graphs with millions of nodes and edges, and discuss several example applications.

Finding suitable, less space consuming views for a document's main content is crucial to provide convenient access to large document collections on display devices of different size. We present a novel compact visualization which represents the document's key semantic as a mixture of images and important key terms, similar to cards in a top trumps game. The key terms are extracted using an advanced text mining approach based on a fully automatic document structure extraction. The images and their captions are extracted using a graphical heuristic and the captions are used for a semi-semantic image weighting. Furthermore, we use the image color histogram for classification and show at least one representative from each non-empty image class. The approach is demonstrated for the IEEE InfoVis publications of a complete year. The method can easily be applied to other publication collections and sets of documents which contain images.